diff --git a/README.md b/README.md index 6c0c325e2..8636333c4 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ Human Brain Project hjorth@kth.se ## Funding -Horizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsrådet (VR-M-2017-02806, VR-M-2020-01652); Swedish e-science Research Center (SeRC); KTH Digital Futures. The computations are enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC KTH partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We acknowledge the use of Fenix Infrastructure resources, which are partially funded from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858. +Horizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsrådet (VR-M-2017-02806, VR-M-2020-01652); Swedish e-science Research Center (SeRC); KTH Digital Futures. The computations are enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC KTH partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We acknowledge the use of Fenix Infrastructure resources, which are partially funded from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858. Snudda is supported and featured on EBRAINS. ## Citation Please cite the first paper for the general Snudda network creation and simulation methods, and the second paper for the Striatal microcircutiry model. diff --git a/examples/notebooks/NEST/Snudda-in-NEST.ipynb b/examples/notebooks/NEST/Snudda-in-NEST.ipynb index fb7b1a222..312bc8968 100644 --- a/examples/notebooks/NEST/Snudda-in-NEST.ipynb +++ b/examples/notebooks/NEST/Snudda-in-NEST.ipynb @@ -20,7 +20,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "07413422-e250-4017-ad0d-13edb2bbf34a", "metadata": { "tags": [] @@ -43,6 +43,7 @@ "from snudda import SnuddaInit\n", "\n", "snudda_data = os.path.join(\"..\", \"..\", \"..\", \"..\", \"BasalGangliaData\", \"data\") # \"/home/hjorth/HBP/BasalGangliaData/data/\" \n", + "snudda_data = \"/home/hjorth/HBP/BasalGangliaData/data/\" \n", "si = SnuddaInit(network_path=network_path, random_seed=12345, snudda_data=snudda_data)\n", "si.define_striatum(num_dSPN=500, num_iSPN=500, num_FS=10, num_LTS=0, num_ChIN=0, neuron_density=80500,\n", " volume_type=\"cube\", neurons_dir=\"$DATA/neurons\")\n", @@ -167,644 +168,12 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "2e229380-8851-4383-ad7c-55c62386235e", "metadata": { - "collapsed": true, - "jupyter": { - "outputs_hidden": true - }, "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Using input file: networks/snudda_in_nest/input-spikes.hdf5\n", - "Copying morphologies\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/morphology/MTC180800A-IDB-cor-rep-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/MTC180800A-IDB-cor-rep-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210/morphology/MTC180800A-IDB-cor-rep-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/MTC180800A-IDB-cor-rep-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var8.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var8.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var4.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var4.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/morphology/MTC180800A-IDB-cor-rep-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/MTC180800A-IDB-cor-rep-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209/morphology/BE104E-cor-rep-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/BE104E-cor-rep-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var4.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var4.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/morphology/MTC180800A-IDB-cor-rep-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/MTC180800A-IDB-cor-rep-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210/morphology/MTC180800A-IDB-cor-rep-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/MTC180800A-IDB-cor-rep-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var4.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var4.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/morphology/WT-P270-09-15ak-cor-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-09-15ak-cor-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var8.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var8.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209/morphology/BE104E-cor-rep-res3-var8.swc to networks/snudda_in_nest/SONATA/components/morphologies/BE104E-cor-rep-res3-var8.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var8.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var8.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210/morphology/DR-rat-Mar-13-08-1-536-R-cor-rep-res3-var8.swc to networks/snudda_in_nest/SONATA/components/morphologies/DR-rat-Mar-13-08-1-536-R-cor-rep-res3-var8.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/morphology/WT-1215MSN03-cor-rep-ax-res3-var4.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-1215MSN03-cor-rep-ax-res3-var4.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/morphology/51-5-DE-cor-rep-ax-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/51-5-DE-cor-rep-ax-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210/morphology/DR-rat-Mar-13-08-1-536-R-cor-rep-res3-var6.swc to networks/snudda_in_nest/SONATA/components/morphologies/DR-rat-Mar-13-08-1-536-R-cor-rep-res3-var6.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var0.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var0.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var4.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var4.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var3.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var3.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/morphology/46-3-DE-cor-rep-ax-res3-var1.swc to networks/snudda_in_nest/SONATA/components/morphologies/46-3-DE-cor-rep-ax-res3-var1.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/morphology/21-6-DE-cor-rep-ax-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/21-6-DE-cor-rep-ax-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/morphology/WT-MSN1-cor-rep-ax-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-MSN1-cor-rep-ax-res3-var7.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var2.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var2.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/morphology/WT-P270-20-15ak-cor-res3-var5.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-P270-20-15ak-cor-res3-var5.swc\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var7.swc to networks/snudda_in_nest/SONATA/components/morphologies/WT-0728MSN01-cor-rep-ax-res3-var7.swc\n", - "Copying mechanisms\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/can_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/Im_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kas_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/can_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kdr_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/tmglut.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/bk_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/caldyn_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cal13_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kaf_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/car_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/im_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/naf_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/par_ggap.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cap_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kaf_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/sk_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/tmglut_double.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kdb_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cat32_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kir_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cal12_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/NO.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kir23_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kv2_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kaf_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/naf_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kir23_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/hcn12_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cadyn_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kas_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/na2_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cal_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kdr_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/car_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/bk_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kv4_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cat33_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/tmgabaa.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kir2_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/caq_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/naf_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/na_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/bk_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/cadyn_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/caq_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/ca_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/vecevent.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kdrb_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/hd_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kcnq_ch.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/sk_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/tmglut_M1RH_D1.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/na3_lts.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/sk_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kdr_fs.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/kir_ms.mod\n", - "Copying /home/hjorth/HBP/BasalGangliaData/data/neurons/mechanisms/it_lts.mod\n", - "Copying hoc files...\n", - "Creating nodes/FS\n", - "Creating nodes/dSPN\n", - "Creating nodes/iSPN\n", - "Missing hoc template: \n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/FS.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/dSPN.json\n", - "Missing ../../../../BasalGangliaData/data/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026/dynamics_params.json file, using ../../../../BasalGangliaData/data/nest/models/iSPN.json\n", - "Writing networks/snudda_in_nest/SONATA/simulation_config.json\n", - "SONATA files exported to networks/snudda_in_nest/SONATA\n" - ] - } - ], + "outputs": [], "source": [ "from snudda.utils.export_sonata import ExportSonata\n", "se = ExportSonata(network_path=network_path)" @@ -836,51 +205,12 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "711e8a95-daf2-4766-aa78-b98351dac708", "metadata": { "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - " -- N E S T --\n", - " Copyright (C) 2004 The NEST Initiative\n", - "\n", - " Version: 3.4.0-post0.dev0\n", - " Built: May 12 2023 11:42:17\n", - "\n", - " This program is provided AS IS and comes with\n", - " NO WARRANTY. See the file LICENSE for details.\n", - "\n", - " Problems or suggestions?\n", - " Visit https://www.nest-simulator.org\n", - "\n", - " Type 'nest.help()' to find out more about NEST.\n", - "\n", - "\n", - "May 16 09:11:56 SimulationManager::set_status [Info]: \n", - " Temporal resolution changed from 0.1 to 0.1 ms.\n" - ] - }, - { - "ename": "NESTErrors.map::at", - "evalue": "map::at in SLI function ConnectSonata_D: C++ exception: map::at", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mNESTErrors.map::at\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[3], line 12\u001b[0m\n\u001b[1;32m 9\u001b[0m sonata_net \u001b[38;5;241m=\u001b[39m nest\u001b[38;5;241m.\u001b[39mSonataNetwork(net_config, sim_config)\n\u001b[1;32m 10\u001b[0m \u001b[38;5;66;03m# node_collections = sonata_net.Create()\u001b[39;00m\n\u001b[0;32m---> 12\u001b[0m node_collections \u001b[38;5;241m=\u001b[39m \u001b[43msonata_net\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mBuildNetwork\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 14\u001b[0m s_rec_dspn \u001b[38;5;241m=\u001b[39m nest\u001b[38;5;241m.\u001b[39mCreate(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mspike_recorder\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 15\u001b[0m s_rec_ispn \u001b[38;5;241m=\u001b[39m nest\u001b[38;5;241m.\u001b[39mCreate(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mspike_recorder\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "File \u001b[0;32m~/NEST/nest-simulator/nest-install/lib/python3.9/site-packages/nest/lib/hl_api_sonata.py:671\u001b[0m, in \u001b[0;36mSonataNetwork.BuildNetwork\u001b[0;34m(self, hdf5_hyperslab_size)\u001b[0m\n\u001b[1;32m 668\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_verify_hyperslab_size(hdf5_hyperslab_size)\n\u001b[1;32m 670\u001b[0m node_collections \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mCreate()\n\u001b[0;32m--> 671\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mConnect\u001b[49m\u001b[43m(\u001b[49m\u001b[43mhdf5_hyperslab_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mhdf5_hyperslab_size\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 673\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m node_collections\n", - "File \u001b[0;32m~/NEST/nest-simulator/nest-install/lib/python3.9/site-packages/nest/lib/hl_api_sonata.py:485\u001b[0m, in \u001b[0;36mSonataNetwork.Connect\u001b[0;34m(self, hdf5_hyperslab_size)\u001b[0m\n\u001b[1;32m 483\u001b[0m sps(graph_specs)\n\u001b[1;32m 484\u001b[0m sps(hdf5_hyperslab_size)\n\u001b[0;32m--> 485\u001b[0m \u001b[43msr\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mConnectSonata\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_is_network_built \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n", - "File \u001b[0;32m~/NEST/nest-simulator/nest-install/lib/python3.9/site-packages/nest/ll_api.py:104\u001b[0m, in \u001b[0;36mcatching_sli_run\u001b[0;34m(cmd)\u001b[0m\n\u001b[1;32m 101\u001b[0m engine\u001b[38;5;241m.\u001b[39mrun(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mclear\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 103\u001b[0m exceptionCls \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mgetattr\u001b[39m(kernel\u001b[38;5;241m.\u001b[39mNESTErrors, errorname)\n\u001b[0;32m--> 104\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exceptionCls(commandname, message)\n", - "\u001b[0;31mNESTErrors.map::at\u001b[0m: map::at in SLI function ConnectSonata_D: C++ exception: map::at" - ] - } - ], + "outputs": [], "source": [ "import nest\n", "\n", @@ -907,6 +237,31 @@ "nest.Connect(node_collections[\"FS\"], s_rec_fs)" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "37ca25ad-6dd5-471e-84a4-a251a3bf49ee", + "metadata": {}, + "outputs": [], + "source": [ + "# If we need to add separate noise. \n", + "# Currently the SONATA specified inputs exist (but according to SONATA documentation it should target virtual neurons), but are not properly connected.\n", + "\n", + "exc_rate = 4.5\n", + "\n", + "exc_noise_fs = nest.Create('poisson_generator', 1300)\n", + "exc_noise_dspn = nest.Create('poisson_generator', 1500)\n", + "exc_noise_ispn = nest.Create('poisson_generator', 1050)\n", + "\n", + "exc_noise_fs.set(rate=exc_rate)\n", + "exc_noise_dspn.set(rate=exc_rate)\n", + "exc_noise_ispn.set(rate=exc_rate)\n", + "\n", + "nest.Connect(exc_noise_fs, node_collections[\"FS\"], 'all_to_all', {'weight': +0.5})\n", + "nest.Connect(exc_noise_dspn, node_collections[\"dSPN\"], 'all_to_all', {'weight': +0.5})\n", + "nest.Connect(exc_noise_ispn, node_collections[\"iSPN\"], 'all_to_all', {'weight': +0.5})" + ] + }, { "cell_type": "code", "execution_count": null, @@ -930,6 +285,24 @@ "nest.raster_plot.from_device(s_rec_fs)\n", "plt.show()" ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9422d804-ff98-4703-b5de-b36af887b8d8", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "121b8022-25cf-45fc-bdb3-5d77c89ccca5", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { diff --git a/examples/parallel/KTH_PDC/Dardel_runSnudda.job b/examples/parallel/KTH_PDC/Dardel_runSnudda.job index a13cfc142..1a856b636 100644 --- a/examples/parallel/KTH_PDC/Dardel_runSnudda.job +++ b/examples/parallel/KTH_PDC/Dardel_runSnudda.job @@ -4,7 +4,7 @@ #SBATCH -e log/runSnudda-%j-error.txt #SBATCH -t 00:30:00 #SBATCH -J Snudda -#SBATCH -A snic2022-5-245 +#SBATCH -A naiss2023-5-231 #SBATCH --nodes=2 #SBATCH -n 256 #SBATCH --cpus-per-task=2 diff --git a/examples/parallel/KTH_PDC/Dardel_simulate.job b/examples/parallel/KTH_PDC/Dardel_simulate.job index 6eb859689..46a1fa5aa 100644 --- a/examples/parallel/KTH_PDC/Dardel_simulate.job +++ b/examples/parallel/KTH_PDC/Dardel_simulate.job @@ -5,7 +5,7 @@ #SBATCH -t 1:59:00 #SBATCH --time-min=1:59:00 #SBATCH -J Simulate -#SBATCH -A snic2022-5-245 +#SBATCH -A naiss2023-5-231 #SBATCH --nodes=1-10 #SBATCH --tasks-per-node=128 #SBATCH --mail-type=ALL diff --git a/snudda/__init__.py b/snudda/__init__.py index b8415a474..66fdcf187 100644 --- a/snudda/__init__.py +++ b/snudda/__init__.py @@ -1,6 +1,6 @@ from .core import Snudda -__version__ = "1.4.7" +__version__ = "1.4.71" from .init import SnuddaInit from .place import SnuddaPlace diff --git a/snudda/data/nest/synapses/excitatory.json b/snudda/data/nest/synapses/excitatory.json new file mode 100644 index 000000000..439852706 --- /dev/null +++ b/snudda/data/nest/synapses/excitatory.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 1 +} diff --git a/snudda/data/nest/synapses/excitatory_distal.json b/snudda/data/nest/synapses/excitatory_distal.json new file mode 100644 index 000000000..2b9fe7d82 --- /dev/null +++ b/snudda/data/nest/synapses/excitatory_distal.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 5 +} diff --git a/snudda/data/nest/synapses/excitatory_proximal.json b/snudda/data/nest/synapses/excitatory_proximal.json new file mode 100644 index 000000000..588bd735f --- /dev/null +++ b/snudda/data/nest/synapses/excitatory_proximal.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 3 +} diff --git a/snudda/data/nest/synapses/excitatory_soma.json b/snudda/data/nest/synapses/excitatory_soma.json new file mode 100644 index 000000000..439852706 --- /dev/null +++ b/snudda/data/nest/synapses/excitatory_soma.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 1 +} diff --git a/snudda/data/nest/synapses/inhibitory.json b/snudda/data/nest/synapses/inhibitory.json new file mode 100644 index 000000000..6f60346f7 --- /dev/null +++ b/snudda/data/nest/synapses/inhibitory.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 2 +} diff --git a/snudda/data/nest/synapses/inhibitory_distal.json b/snudda/data/nest/synapses/inhibitory_distal.json new file mode 100644 index 000000000..4f6614245 --- /dev/null +++ b/snudda/data/nest/synapses/inhibitory_distal.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 6 +} diff --git a/snudda/data/nest/synapses/inhibitory_proximal.json b/snudda/data/nest/synapses/inhibitory_proximal.json new file mode 100644 index 000000000..5ea1a2837 --- /dev/null +++ b/snudda/data/nest/synapses/inhibitory_proximal.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 4 +} diff --git a/snudda/data/nest/synapses/inhibitory_soma.json b/snudda/data/nest/synapses/inhibitory_soma.json new file mode 100644 index 000000000..6f60346f7 --- /dev/null +++ b/snudda/data/nest/synapses/inhibitory_soma.json @@ -0,0 +1,3 @@ +{ + "receptor_type": 2 +} diff --git a/snudda/plotting/Blender/visualisation/visualise_network.py b/snudda/plotting/Blender/visualisation/visualise_network.py index 17c3990f0..81783a951 100644 --- a/snudda/plotting/Blender/visualisation/visualise_network.py +++ b/snudda/plotting/Blender/visualisation/visualise_network.py @@ -16,11 +16,13 @@ class VisualiseNetwork(object): # You need to provide neuron def __init__(self, network_path, blender_save_file=None, blender_output_image=None, - network_json=None, simulation_output_file_name=None): + network_json=None, simulation_output_file_name=None, use_neuron_cache=True): self.network_path = network_path self.snudda_data = get_snudda_data(network_path=network_path) self.scale_f = 1000 # factor to downscale the data + self.neuron_colour_lookup = dict() # Allow the user to override the neuron colours + self.use_neuron_cache = use_neuron_cache if network_json: self.network_json = network_json @@ -54,11 +56,22 @@ def __init__(self, network_path, blender_save_file=None, blender_output_image=No self.sl.import_json(self.network_json) self.data = self.sl.data + def set_neuron_colour(self, neuron_id, colour): + + if len(colour) != 4: + raise ValueError(f"Colour should be R,G,B,alpha (4 values)") + self.neuron_colour_lookup[neuron_id] = colour + + def clear_neuron_colours(self): + + self.neuron_colour_lookup = dict() + def visualise(self, neuron_id=None, blender_output_image=None, white_background=True, show_synapses=True, + synapse_colour=None, synapse_pair_filter=None, draw_meshes=True, full_meshes=None, @@ -75,6 +88,7 @@ def visualise(self, blender_output_image white_background show_synapses + synapse_colour: R,G,B,alpha (For values, range 0-1). Default None. synapse_pair_filter (list): List of pairs of neurons (tuples) to show synapses for, default None = no filtering camera_location camera_rotation @@ -83,7 +97,7 @@ def visualise(self, """ - if neuron_id: + if neuron_id is not None: neurons = [self.data["neurons"][x] for x in neuron_id] else: neurons = self.data["neurons"] @@ -140,6 +154,14 @@ def visualise(self, bg.inputs[0].default_value[:3] = (0.0, 0.0, 0.0) bg.inputs[1].default_value = 0.0 + #Scott's magic + ''' + mat_dspn = bpy.data.materials.new("DSPN") + mat_dspn.use_nodes = True + mat_dspn.node_tree.nodes["Principled BSDF"].inputs[0].default_value = (0, 1, 0, 1) + mat_dspn.node_tree.nodes["Principled BSDF"].inputs['Alpha'].default_value = 1 + ''' + # Define materials mat_dspn = bpy.data.materials.new("PKHG") mat_dspn.diffuse_color = (77. / 255, 151. / 255, 1.0, 0.5) @@ -184,12 +206,29 @@ def visualise(self, "synapse": mat_synapse, "other": mat_other} - if white_background: + # Add the user requested custom colours + for nid in self.neuron_colour_lookup.keys(): + material_lookup[nid] = bpy.data.materials.new(str(nid)) + material_lookup[nid].use_nodes = True + material_lookup[nid].node_tree.nodes["Principled BSDF"].inputs[0].default_value = self.neuron_colour_lookup[nid] + material_lookup[nid].node_tree.nodes["Principled BSDF"].inputs['Alpha'].default_value = self.neuron_colour_lookup[nid][-1] + + #material_lookup[nid] = bpy.data.materials.new("PKHG") + #material_lookup[nid].diffuse_color = self.neuron_colour_lookup[nid] + + if synapse_colour is not None: + mat_synapse.diffuse_color = synapse_colour + elif white_background: mat_synapse.diffuse_color = (0.8, 0.0, 0.0, 1.0) else: mat_synapse.diffuse_color = (1.0, 1.0, 0.9, 1.0) # matSynapse.use_transparency = True + + """ + # We comment out these lines, to get the synapse colour to be set correctly (otherwise they are white) + # Thanks Scott for finding this fix. + mat_synapse.use_nodes = True if not white_background: @@ -201,12 +240,13 @@ def visualise(self, material_output = mat_synapse.node_tree.nodes.get('Material Output') mat_synapse.node_tree.links.new(material_output.inputs[0], emission.outputs[0]) + """ - for neuron in neurons: + for idx, neuron in enumerate(neurons): e_rot = mathutils.Matrix(neuron["rotation"].reshape(3, 3)).to_euler() - if neuron["name"] in self.neuron_cache: + if self.use_neuron_cache and neuron["name"] in self.neuron_cache: # If we already have the object in memory, copy it. obj = self.neuron_cache[neuron["name"]].copy() @@ -220,7 +260,15 @@ def visualise(self, obj.name = f"{neuron['name']}-{neuron['neuronID']}" VisualiseNetwork.link_object(obj) else: - self.read_swc_data(filepath=snudda_parse_path(neuron["morphology"], self.snudda_data), detail_level=detail_level) + if type(detail_level) == np.ndarray: + if len(detail_level) != len(neurons): + raise ValueError(f"detail_level is either 1,2 or 3, " + f"if given as a array must be same length as number of neurons (ie {len(idx)}).") + dl = detail_level[idx] + else: + dl = detail_level + + self.read_swc_data(filepath=snudda_parse_path(neuron["morphology"], self.snudda_data), detail_level=dl) obj = bpy.context.selected_objects[0] obj.name = f"{neuron['name']}-{neuron['neuronID']}" @@ -233,7 +281,11 @@ def visualise(self, n_type = neuron["type"].lower() - if n_type in material_lookup: + if neuron['neuronID'] in material_lookup: + # Custom colour for neuron (priority) + mat = material_lookup[neuron['neuronID']] + elif n_type in material_lookup: + # Each neuron type has its own colour mat = material_lookup[n_type] else: mat = material_lookup["other"] diff --git a/snudda/utils/ablate_network.py b/snudda/utils/ablate_network.py index 5985c0c42..af9b1f0e8 100755 --- a/snudda/utils/ablate_network.py +++ b/snudda/utils/ablate_network.py @@ -136,6 +136,9 @@ def filter_synapses(self, data_type): synapse_data = self.in_file[f"network/{data_type}"][()].copy() + if synapse_data.size == 0: + return np.array([], dtype=int) + keep_flag = np.zeros((synapse_data.shape[0],), dtype=bool) # Shortcut, if user wants to remove all, skip the processing part @@ -354,10 +357,15 @@ def write_network(self, out_file_name=None, print_remapping=False): row[1] = remap_id[row[1]] temp_gj_mat[idx, :] = row + if temp_gj_mat.size > 0: + gj_chunk_size = self.in_file["network/gapJunctions"].chunks + else: + gj_chunk_size = None + network_group.create_dataset("gapJunctions", data=temp_gj_mat, dtype=np.int32, shape=(num_gj, self.in_file["network/gapJunctions"].shape[1]), - chunks=self.in_file["network/gapJunctions"].chunks, + chunks=gj_chunk_size, maxshape=(None, self.in_file["network/gapJunctions"].shape[1]), compression=self.in_file["network/gapJunctions"].compression) diff --git a/snudda/utils/conv_hurt.py b/snudda/utils/conv_hurt.py index 4463030bf..aaddcee45 100644 --- a/snudda/utils/conv_hurt.py +++ b/snudda/utils/conv_hurt.py @@ -13,7 +13,7 @@ class ConvHurt(object): - def __init__(self, simulation_structures, base_dir="TEST/", target_simulator="NEST"): + def __init__(self, simulation_structures, base_dir="TEST/", target_simulator="NEST", has_input=False): self.base_dir = base_dir self.network_dir = os.path.join(base_dir, 'networks') @@ -25,7 +25,7 @@ def __init__(self, simulation_structures, base_dir="TEST/", target_simulator="NE self.setup_directories(base_dir=base_dir) self.write_main_config(simulation_structures=simulation_structures, - base_dir=base_dir, target_simulator=target_simulator) + base_dir=base_dir, target_simulator=target_simulator, has_input=has_input) ############################################################################ @@ -66,7 +66,8 @@ def write_main_config(self, base_dir="TEST/", out_file="circuit_config.json", simulation_structures=[], - target_simulator="NEURON"): + target_simulator="NEURON", + has_input=False): config = OrderedDict([]) @@ -102,6 +103,15 @@ def write_main_config(self, "edge_types_file": os.path.join("$NETWORK_DIR", f"{ss}_edge_types.csv") } edges.append(edge_info) + if has_input: + node_info = {"nodes_file": os.path.join("$NETWORK_DIR", f"{ss}-input_nodes.hdf5"), + "node_types_file": os.path.join("$NETWORK_DIR", f"{ss}-input_node_types.csv")} + nodes.append(node_info) + + edge_info = {"edges_file": os.path.join("$NETWORK_DIR", f"{ss}-input_edges.hdf5"), + "edge_types_file": os.path.join("$NETWORK_DIR", f"{ss}-input_edge_types.csv")} + edges.append(edge_info) + config["networks"] = OrderedDict([("nodes", nodes), ("edges", edges)]) with open(os.path.join(base_dir, out_file), 'wt') as f: @@ -361,23 +371,23 @@ def write_edges_csv(self, ############################################################################ - def write_input(self, spike_file_name, spikes): - - if spikes is None: - print(f"No spikes specified, not writing {spike_file_name}") - print("Use python3 Network_input.py yourinput.json yournetwork.hdf5 input-spikes.hdf5") - return + def write_input(self, spike_file_name, spike_times, gids): f_name = os.path.join(self.base_dir, spike_file_name) + print(f"Writing spikes to {f_name}") + with h5py.File(f_name, 'w', libver=self.h5py_libver) as f: self.add_version(f) print(f"Writing file {f_name}") s_group = f.create_group("spikes") - s_group.create_dataset("gids", data=spikes[:, 1]) - s_group.create_dataset("timestamps", data=spikes[:, 0]) + s_group.attrs["sorting"] = "gid" + s_group.create_dataset("gids", data=gids) + s_group.create_dataset("timestamps", data=spike_times*1e3) # Convert to ms + + return f_name ############################################################################ @@ -405,65 +415,3 @@ def add_version(self, hdf5_file): hdf5_file.attrs["version"] = [0, 1] hdf5_file.attrs["magic"] = 0x0A7A - - -if __name__ == "__main__": - # ch = ConvHurt() - # ch = ConvHurt(simulationStructure="cerebellum", - # inputStructures=["pons","cortex"]) - - ch = ConvHurt(simulation_structure="striatum", - input_structures=["cortex", "thalamus"]) - - # Test example, we have 5 neurons, big network - # two groups - - node_data = {"positions": np.array([[1., 2., 3.], [4., 5., 6.], [7., 8., 9.], - [1., 8., 9.], [2., 3., 2.]]), - "rotation_angle_zaxis": np.array([0.1, 0.2, 0.3, 0.4, 0.5])} - - ch.write_nodes(node_file='striatum_nodes.hdf5', - data=node_data, - node_id=np.array([0, 1, 2, 3, 4]), - population_name="striatum_nodes", - node_type_id=np.array([0, 1, 0, 1, 0]), - node_group_id=np.array([0, 0, 1, 1, 1]), - node_group_index=np.array([0, 1, 0, 1, 2])) - - node_type_id = np.array([0, 1]) - node_data_csv = OrderedDict([('name', ['A', 'B']), - ('location', ['structA', 'structB'])]) - - ch.write_node_csv(node_csv_file='striatum_node_types.csv', - node_type_id=node_type_id, - data=node_data_csv) - - edge_group = np.array([5, 5, 11, 11, 11]) - edge_group_index = np.array([0, 1, 0, 1, 2]) - edge_type_id = np.array([0, 1, 0, 1, 0]) - source_gid = np.array([1, 2, 3, 3, 4]) - target_gid = np.array([2, 3, 4, 0, 1]) # THESE ARE SORTED ... HAHAHA - - # Delay needs to be in ms (bad bad people, real scientists use SI units) - edge_data = OrderedDict([("sec_id", np.array([10, 22, 33, 24, 15])), - ("sec_x", np.array([0.1, 0.3, 0.5, 0.2, 0])), - ("syn_weight", np.array([0.1e-9, 2e-9, 3e-9, - 0.3e-9, 0.1e-9])), - ("delay", 1e3 * np.array([1e-3, 4e-3, 2e-3, 5e-3, 1e-3]))]) - - ch.write_edges(edge_file="striatum_edges.hdf5", - edge_group=edge_group, - edge_group_index=edge_group_index, - edge_type_id=edge_type_id, - edge_population_name="striatum_edges", - source_id=source_gid, - target_id=target_gid, - data=edge_data) - - edge_type_id = np.array([0, 1]) - edge_csv_data = OrderedDict([('template', ['Exp2Syn', 'NULL']), - ('dynamics_params', ["mysyn.json", 'yoursyn.json'])]) - - ch.write_edges_csv(edge_csv_file="striatum_edge_types.csv", - edge_type_id=edge_type_id, - data=edge_csv_data) diff --git a/snudda/utils/export_sonata.py b/snudda/utils/export_sonata.py index b4a5d4ca4..a50866569 100644 --- a/snudda/utils/export_sonata.py +++ b/snudda/utils/export_sonata.py @@ -2,6 +2,7 @@ # # TODO: +# - Add support for gap junctions # - Check what axon and dendrite propagation speeds should be # @@ -59,7 +60,12 @@ def __init__(self, network_path=None, network_file=None, input_file=None, out_di self.network_config = json.loads(self.snudda_load.data["config"]) - print(f"Using input file: {self.input_file}") + if self.input_file: + print(f"Using input file: {self.input_file}") + has_input = True + else: + print("No input file specified, and default file not found.") + has_input = False # This contains data for converting to Neurodamus secID and secX self.morph_cache = dict([]) @@ -71,7 +77,7 @@ def __init__(self, network_path=None, network_file=None, input_file=None, out_di # TODO: We need to read structure names from the network-config.json structure_names = [x for x in self.network_config["Volume"]] ch = ConvHurt(simulation_structures=structure_names, - base_dir=self.out_dir) + base_dir=self.out_dir, has_input=has_input) self.copy_morphologies() self.copy_mechanisms() @@ -106,14 +112,22 @@ def __init__(self, network_path=None, network_file=None, input_file=None, out_di if self.target_simulator == "NEST": if "nestModelTemplate" in con_type_data["channelParameters"]: edge_model = con_type_data["channelParameters"]["nestModelTemplate"] + if "nestDynamicParams" not in con_type_data["channelParameters"]: + raise KeyError("If nestModelTemplate is specified, nestDynamicParams must be specified also") + dynamic_params = con_type_data["channelParameters"]["nestDynamicParams"] else: edge_model = "static_synapse" + if con_type == "GABA": + dynamic_params = "inhibitory.json" + else: + dynamic_params = "excitatory.json" else: edge_model = con_type_data["channelParameters"]["modFile"] - edge_type_lookup[pre_type, post_type, con_type] = (edge_type_id, edge_model, f"{pre_type}_{post_type}") + edge_type_lookup[pre_type, post_type, con_type] = (edge_type_id, edge_model, f"{pre_type}_{post_type}", dynamic_params) node_id_remap = np.full(shape=(self.snudda_load.data["nNeurons"],), fill_value=-1, dtype=int) + input_list = [] for volume_name in volume_list: @@ -194,26 +208,142 @@ def __init__(self, network_path=None, network_file=None, input_file=None, out_di edge_type_id = [x[0] for x in edge_type_lookup.values()] - edge_data = {"model_template": [x[1] for x in edge_type_lookup.values()], - "population": [x[2] for x in edge_type_lookup.values()]} + edge_data_csv = {"model_template": [x[1] for x in edge_type_lookup.values()], + "population": [x[2] for x in edge_type_lookup.values()], + "dynamic_params": [x[3] for x in edge_type_lookup.values()]} ch.write_edges_csv(edge_csv_file=f"{volume_name}_edge_types.csv", edge_type_id=edge_type_id, - data=edge_data) + data=edge_data_csv) + + if self.input_file: + + (sonata_input_hdf5, + sonata_virtual_node_hdf5, sonata_virtual_node_csv, + sonata_virtual_edges_hdf5, sonata_virtual_edges_csv) = \ + self.write_input(node_id_remap=node_id_remap, + input_hdf5=self.input_file, + conv_hurt=ch, volume_name=volume_name) - # !!! WE ALSO NEED TO ADD BACKGROUND INPUT TO THE NEURONS IN THE NETWORK + input_list.append((volume_name, sonata_input_hdf5, + sonata_virtual_node_hdf5, sonata_virtual_node_csv, + sonata_virtual_edges_hdf5, sonata_virtual_edges_csv)) - self.write_simulation_config() + # !!! TODO: We need to pass the new input files, node and edge files to the config + self.write_simulation_config(input_list=input_list) print(f"SONATA files exported to {self.out_dir}") ############################################################################ - def get_edge_type_lookup(self): + def get_all_input_types(self, input_hdf5, neuron_type=None, volume_name=None): - # Read the config file, to find out all possible types of connections + input_types = set() - pass + if type(input_hdf5) != h5py._hl.files.File: + input_hdf5 = h5py.File(input_hdf5, "r") + + neuron_id_list = self.snudda_load.get_neuron_id_of_type(neuron_type=neuron_type, volume=volume_name) + + for neuron_id in neuron_id_list: + neuron_input_types = set(input_hdf5[f"input/{neuron_id}"].keys()) + + input_types += neuron_input_types + + return input_types + + def write_input(self, + input_hdf5, + conv_hurt, + node_id_remap, + volume_name=None): + + """ + Args: + input_hdf5 : File to read data from + sonata_input_hdf5 : File to write data to + conv_hurt : + node_id_remap : Numpy array mapping neuron_id to gid (which is population specific) + volume_name (str) : Name of volume (default: None, assumes neuron type only in one volume) + """ + + # If there are N neurons in the volume, and they receive cortical and thalamic input + # + # Then... + # Virtual neuron 0-(N-1) provide cortical input to neurons 0-(N-1) + # Virtual neuron N-(2*N-1) provide thalamic input to neurons 0-(N-1) + # + + if type(input_hdf5) != h5py._hl.files.File: + input_hdf5 = h5py.File(input_hdf5, "r") + + sonata_input_hdf5 = f"inputs/input_{volume_name}.hdf5" + + neuron_id_list = self.snudda_load.get_neuron_id_of_type(volume=volume_name, neuron_type=None) + input_data = [] # [(neuron_type, neuron_node_id, input_type, spikes, weight, virtual_node_id), (np, nid, it, s, w, vid), ...] + + virtual_node_ctr = 0 + + for neuron_id in neuron_id_list: + + for input_type in input_hdf5[f"input/{neuron_id}"].keys(): + neuron_spikes = [] + + spike_group = input_hdf5[f"input/{neuron_id}/{input_type}/spikes"] + n_spikes = spike_group.attrs["nSpikes"] + + for idx, ns in enumerate(n_spikes): + neuron_spikes.append(spike_group[idx, :ns]) + + input_spikes = np.array(sorted(np.concatenate(neuron_spikes))) + + neuron_type = self.snudda_load.data["neurons"][neuron_id]["type"] + + weight = input_hdf5[f"input/{neuron_id}/{input_type}"].attrs["conductance"] * 1e6 # microsiemens for NEST + if "GABA" in input_hdf5[f"input/{neuron_id}/{input_type}"].attrs["modFile"].upper(): + weight *= -1 + + # [(neuron_type, neuron_node_id, input_type, spikes, weight, virtual_node_id), (np, nid, it, s, w, vid), ...] + input_data.append((neuron_type, node_id_remap[neuron_id], input_type, input_spikes, weight, virtual_node_ctr)) + virtual_node_ctr += 1 + + # Next we need to write the input spikes to file + all_spikes = [] + all_gid = [] + + for _, _, _, spikes, _, gid in input_data: + all_spikes.append(spikes) + all_gid.append(np.full(shape=spikes.shape, fill_value=gid, dtype=int)) + + spikes = np.concatenate(all_spikes) + gids = np.concatenate(all_gid) + + if len(spikes) == 0: + return None + + # We need to make sure the spikes are sorted by gid, then by time + idx = np.lexsort((spikes, gids)) + + f_name = conv_hurt.write_input(spike_file_name=sonata_input_hdf5, + spike_times=spikes[idx], + gids=gids[idx]) + + input_hdf5.close() + + # We also need to create the virtual nodes, and edges to connect them + + virtual_node_id = np.array([x[5] for x in input_data], dtype=int) + neuron_type = [x[0] for x in input_data] + node_id = np.array([x[1] for x in input_data], dtype=int) + weight = np.array([x[4] for x in input_data]) + + sonata_virtual_node_hdf5, sonata_virtual_node_csv, sonata_virtual_edges_hdf5, sonata_virtual_edges_csv = \ + self.add_virtual_input(volume_name=volume_name, virtual_node_id=virtual_node_id, + neuron_type=neuron_type, node_id=node_id, weight=weight, conv_hurt=conv_hurt) + + return (sonata_input_hdf5, + sonata_virtual_node_hdf5, sonata_virtual_node_csv, + sonata_virtual_edges_hdf5, sonata_virtual_edges_csv) ############################################################################ @@ -370,7 +500,6 @@ def allocate_groups_and_remap_nodeid(self): return node_group_id, group_idx, group_lookup, neuron_id_remap - def remap_nodes(self): n_neurons = self.snudda_load.data["nNeurons"] @@ -499,6 +628,45 @@ def setup_edge_population(self, node_group_lookup): ############################################################################ + def get_nest_synapse_models(self): + + synapse_model_lookup = dict() + + for synapse_models in self.snudda_load.data["connectivityDistributions"].values(): + for synapse_type, synapse_model in synapse_models.items(): + synapse_type_id = synapse_model["channelModelID"] + + if synapse_type == "GABA": + synapse_model_lookup[synapse_type_id] = dict() + synapse_model_lookup[synapse_type_id]["soma"] = "inhibitory_soma.json" + synapse_model_lookup[synapse_type_id]["proximal"] = "inhibitory_proximal.json" + synapse_model_lookup[synapse_type_id]["distal"] = "inhibitory_distal.json" + else: + # Assume excitatory + synapse_model_lookup[synapse_type_id] = dict() + synapse_model_lookup[synapse_type_id]["soma"] = "excitatory_soma.json" + synapse_model_lookup[synapse_type_id]["proximal"] = "excitatory_proximal.json" + synapse_model_lookup[synapse_type_id]["distal"] = "excitatory_distal.json" + + return synapse_model_lookup + + def get_nest_synapse_sign_lookup(self): + + synapse_sign_lookup = dict() + + for synapse_models in self.snudda_load.data["connectivityDistributions"].values(): + for synapse_type, synapse_model in synapse_models.items(): + synapse_type_id = synapse_model["channelModelID"] + + if synapse_type.upper() == "GABA": + synapse_sign_lookup[synapse_type_id] = -1.0 + else: + synapse_sign_lookup[synapse_type_id] = 1.0 + + return synapse_sign_lookup + + ############################################################################ + # This code sets up the info about edges def setup_edge_info(self, edge_population_lookup, node_group_id, group_idx): @@ -524,6 +692,8 @@ def setup_edge_info(self, edge_population_lookup, node_group_id, group_idx): # 4: locType, 5: synapseType, 6: somaDistDend 7:somaDistAxon # somaDist is an int, representing micrometers + synapse_sign_lookup = self.get_nest_synapse_sign_lookup() + for i_syn, syn_row in enumerate(self.snudda_load.data["synapses"]): source_gid[i_syn] = group_idx[syn_row[0]] target_gid[i_syn] = group_idx[syn_row[1]] @@ -541,6 +711,11 @@ def setup_edge_info(self, edge_population_lookup, node_group_id, group_idx): sec_id[i_syn] = syn_row[9] sec_x[i_syn] = syn_row[10] / 1000.0 synapse_type = syn_row[6] + synapse_conductance = syn_row[11] * 1e-3 # pS --> micro simens + + # We need to set the weight to negative for inhibitory synapses it seems + # hence the synapse_sign_lookup (returns +1 or -1) + syn_weight[i_syn] = synapse_conductance * synapse_sign_lookup[synapse_type] pre_type = self.snudda_load.data["neurons"][source_gid[i_syn]]["type"] post_type = self.snudda_load.data["neurons"][target_gid[i_syn]]["type"] @@ -550,7 +725,6 @@ def setup_edge_info(self, edge_population_lookup, node_group_id, group_idx): dend_dist = syn_row[6] * 1e-6 axon_dist = syn_row[7] * 1e-6 delay[i_syn] = axon_dist / axon_speed * 1e3 + 1 # Delay in ms and not SI units :-( - syn_weight[i_syn] = 1.0 # !!! THIS NEEDS TO BE SET DEPENDING ON CONNECTION TYPE edge_data = OrderedDict([("afferent_section_id", sec_id), ("afferent_section_pos", sec_x), @@ -830,7 +1004,7 @@ def plot_section_data(self, morph, swc_file): ############################################################################ - def write_simulation_config(self): + def write_simulation_config(self, input_list): sim_conf = dict([]) @@ -859,15 +1033,20 @@ def write_simulation_config(self): # node_sets_file contains the reports we want written from the simulation # simConf["node_sets_file"] = None # !!! THIS NEEDS TO BE WRITTEN - cortex_input = {"input_type": "spikes", - "module": "h5", - "input_file": "$INPUT_DIR/cortexInput.hdf5"} + if input_list: + sim_conf["inputs"] = dict() - thalamus_input = {"input_type": "spikes", - "module": "h5", - "input_file": "$INPUT_DIR/thalamusInput.hdf5"} - sim_conf["inputs"] = {"cortexInput": cortex_input, - "thalamusInput": thalamus_input} + for volume_name, sonata_input_hdf5, \ + sonata_virtual_node_hdf5, sonata_virtual_node_csv, \ + sonata_virtual_edges_hdf5, sonata_virtual_edges_csv in input_list: + + input_info = dict() + input_info["input_type"] = "spikes" + input_info["module"] = "h5" + input_info["input_file"] = f"$INPUT_DIR/{os.path.basename(sonata_input_hdf5)}" + input_info["node_set"] = f"{volume_name}-input" + + sim_conf["inputs"][f"{volume_name}_spikes"] = input_info out_conf_file = os.path.join(self.out_dir, "simulation_config.json") print(f"Writing {out_conf_file}") @@ -943,10 +1122,25 @@ def copy_mechanisms(self): mech_file = os.path.basename(mech) copyfile(mech, os.path.join(self.out_dir, "components", "mechanisms", mech_file)) + def copy_nest_synapses(self): + print("Copying NEST synapses") + + mech_path = snudda_parse_path(os.path.join("$SNUDDA_DATA", "nest", "synapses"), + snudda_data=self.snudda_load.data["SnuddaData"]) + + for mech in glob(os.path.join(mech_path, "*.json")): + if self.debug: + print(f"Copying {mech}") + + mech_file = os.path.basename(mech) + copyfile(mech, os.path.join(self.out_dir, "components", "synapse_dynamics", mech_file)) + ############################################################################ def sort_input(self, nl, node_type_id_lookup, input_name=None): + raise DeprecationWarning("Code is deprecated") + if self.input_file is None or not os.path.isfile(self.input_file): print("No input file has been specified!") return None @@ -1000,6 +1194,78 @@ def sort_input(self, nl, node_type_id_lookup, input_name=None): ############################################################################ + def add_virtual_input(self, volume_name, virtual_node_id, neuron_type, node_id, weight, conv_hurt): + + """ Creates one virtual neurons, to provide external input to that the neuron population + + To know the target neuron, we need to know both neuron population, and node id within that population + + Args: + volume_name (str): Name of volume + virtual_node_id (np.array): ID of all virtual nodes + neuron_type (list of str): Which population does each input target + node_id (np.array): ID of nodes that are connected + conv_hurt : ConvHurt object + """ + + virtual_neuron_population = f"{volume_name}-input" + virtual_node_file = f"{virtual_neuron_population}_nodes.hdf5" + + n_virtual_nodes = len(virtual_node_id) + node_data = dict() # Let's see if we get away without specifying coordinates + virtual_node_type_id = np.zeros(shape=(n_virtual_nodes, ), dtype=int) + virtual_node_group_id = np.zeros(shape=(n_virtual_nodes, ), dtype=int) + virtual_node_group_index = np.arange(0, n_virtual_nodes, dtype=int) + + conv_hurt.write_nodes(node_file=virtual_node_file, + population_name=virtual_neuron_population, + data=node_data, + node_id=virtual_node_id, + node_type_id=virtual_node_type_id, + node_group_id=virtual_node_group_id, + node_group_index=virtual_node_group_index, + close_file=True) + + csv_virtual_node_types_file = f"{virtual_neuron_population}_node_types.csv" + + virtual_node_data_csv = OrderedDict([("model_type", ["virtual"])]) + conv_hurt.write_node_csv(node_csv_file=csv_virtual_node_types_file, + node_type_id=[0], + data=virtual_node_data_csv) + + edge_file = f"{virtual_neuron_population}_edges.hdf5" + + population_rows = dict() + + # We need to write separate sets of edges for each targeted population + for nrn_type in set(neuron_type): + population_rows[f"{volume_name}-input_{nrn_type}"] = \ + np.array([i for (i, val) in enumerate(neuron_type) if val == nrn_type], dtype=int) + # population_rows[nrn_type] = np.where(np.array(neuron_type) == nrn_type)[0] + + edge_data = {"syn_weight": weight} + + conv_hurt.write_edges(edge_file=edge_file, + population_rows=population_rows, + edge_type_id=np.zeros(len(virtual_node_id), dtype=int), + source_id=virtual_node_id, + target_id=node_id, + data=edge_data) + + edge_types_file_csv = f"{virtual_neuron_population}_edge_types.csv" + edge_type_id = np.array([0]) + edge_data_csv = {"model_template": ["static_synapse"]} + + conv_hurt.write_edges_csv(edge_csv_file=edge_types_file_csv, + edge_type_id=edge_type_id, + data=edge_data_csv) + + return virtual_node_file, csv_virtual_node_types_file, edge_file, edge_types_file_csv + + def add_edges_for_virtual_neurons_input(self): + + pass + ############################################################################ diff --git a/snudda/utils/load.py b/snudda/utils/load.py index 169c10b1c..bc90ec6b5 100755 --- a/snudda/utils/load.py +++ b/snudda/utils/load.py @@ -752,7 +752,7 @@ def get_neuron_id_of_type(self, neuron_type, num_neurons=None, random_permute=Fa """ neuron_id = np.array([x["neuronID"] for x in self.data["neurons"] - if x["type"] == neuron_type and (volume is None or x["volumeID"] == volume)]) + if (neuron_type is None or x["type"] == neuron_type) and (volume is None or x["volumeID"] == volume)]) assert not random_permute or num_neurons is not None, "random_permute is only valid when num_neurons is given" @@ -775,8 +775,9 @@ def get_neuron_id_of_type(self, neuron_type, num_neurons=None, random_permute=Fa print(f"get_neuron_id_of_type: wanted {num_neurons} only got {len(neuron_id)} " f"neurons of type {neuron_type}") - # Double check that all of the same type - assert np.array([self.data["neurons"][x]["type"] == neuron_type for x in neuron_id]).all() + # Double check that all of the same type (or neuron_type is None) + assert neuron_type is None or np.array([self.data["neurons"][x]["type"] == neuron_type for x in neuron_id]).all() + assert volume is None or np.array([self.data["neurons"][x]["volumeID"] == volume for x in neuron_id]).all() return neuron_id diff --git a/tests/test_sonata.py b/tests/test_sonata.py index 9f5a28635..969426d4b 100644 --- a/tests/test_sonata.py +++ b/tests/test_sonata.py @@ -8,6 +8,7 @@ from snudda import SnuddaDetect from snudda import SnuddaPrune from snudda import SnuddaLoad +from snudda.input import SnuddaInput from snudda.utils.export_sonata import ExportSonata from sonata.circuit import File as SonataFile @@ -39,6 +40,10 @@ def setUp(self, create_network=True): sp = SnuddaPrune(network_path=self.network_path) sp.prune() + input_config_file = os.path.join("networks", "network_testing_input","input-test-1.json") + si = SnuddaInput(network_path=self.network_path, input_config_file=input_config_file) + si.generate() + def test_sonata_export(self): network_file = os.path.join(self.network_path, "network-synapses.hdf5") @@ -139,6 +144,7 @@ def test_sonata_export(self): self.assertEqual(edge_count, sl.data["nSynapses"]) self.assertTrue((con_mat == new_con_mat).all()) + # !!! TODO: Add test for input, also write dedicated input.json file for this test if __name__ == '__main__': unittest.main()